0
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2
replies
1.3k
views
CRISPRseek package: findgRNAs error
CRISPRseek
4.2 years ago nderian ▴ 10
0
votes
2
replies
1.2k
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R/Bioconductor package for Circulating Cell-Free DNA data analysis
SequencingData
4.3 years ago • updated 4.2 years ago adR ▴ 40
0
votes
1
reply
1.5k
views
upset-style plot to show marginal intersections
UpsetPlot
updated 4.2 years ago by ▴ 760 • written 4.2 years ago by • 0
0
votes
2
replies
1.6k
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
6
votes
7
replies
3.6k
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GEOquery reading error on Windows.
GEOquery GEO Gene
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 50
0
votes
0
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751
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genbankr throwing C stack usage error when reading in files >500Kb
genbankr
4.2 years ago Lauren • 0
0
votes
5
replies
1.8k
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Is there a way to get the confidence interval for the fold change generated on DESeq2
DESeq2
4.2 years ago adeler001 • 0
4
votes
4
replies
6.8k
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FeatureCounts
counts subread RNASeq featurecounts
4.2 years ago k___ ▴ 30
0
votes
1
reply
1.1k
views
write a for loop for searching TF with TFBSTools
TFBSTools R forloop
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
1
vote
5
replies
2.4k
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slow bplapply?
BiocParallel
4.2 years ago • updated 3.1 years ago Wu, Hao ▴ 20
2
votes
4
replies
1.8k
views
default behaviour of import.bw
import.bw rtracklayer
4.2 years ago Yixin • 0
0
votes
1
reply
1.3k
views
Issue with annotation package mouse4302.db
mouse4302.db annotation
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
1
vote
1
reply
1.7k
views
affycoretools - include percent variance explained in plotPCA()
affycoretools
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 180
1
vote
1
reply
1.1k
views
afffycoretools - warnings in mirna2mrna()
affycoretools DBI
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 180
1
vote
3
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2.8k
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Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
4.2 years ago polemiraza ▴ 70
15
votes
13
replies
4.8k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by ▴ 20
0
votes
2
replies
1.3k
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question about the refined outputs from GOfuncR package
GOfuncR
4.2 years ago • updated 3.6 years ago capricygcapricyg ▴ 10
0
votes
0
replies
1.1k
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Read the first sequence from fasta file - TFBSTool
TFBSTools FASTA RStudio
4.2 years ago HELEN • 0
0
votes
1
reply
1.8k
views
tximport samples with separate tx2gene maps
tximport
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
906
views
DESeq2 Timecourse design
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
3
votes
5
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2.6k
views
Error when using summarizeToGene with tximeta input for DESeq2 analysis
tximeta SummarizedExperiment DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
1
reply
982
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
1
vote
2
replies
1.8k
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Identifying presence of certain genes
DifferentialExpression TCGAWorkflow
4.2 years ago Sam ▴ 10
6
votes
10
replies
2.5k
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rnaseqGene: Different output when generating step by step airway dataset
tximeta DESeq2 rnaseqGene
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 20
0
votes
0
replies
1.3k
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about monocle3
monocle3
4.2 years ago Bogdan ▴ 670
3
votes
4
replies
3.8k
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STRINGdb: Error in download.file(urlStr, temp)
STRINGdb R
updated 4.0 years ago by ▴ 110 • written 4.2 years ago by ▴ 10
0
votes
2
replies
2.6k
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Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 4.2 years ago by ▴ 450 • written 4.2 years ago by • 0
0
votes
1
reply
1.4k
views
TFBSTools and readFASTA
TFBSTools DNASeqData readFASTA DNA RStudio
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
2
votes
5
replies
2.1k
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Extracting fitted expression in limma
limma
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
2
votes
3
replies
1.7k
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slidingIRanges in IRanges ... odd behavior
IRanges
updated 3.0 years ago by • 0 • written 4.2 years ago by ▴ 20
0
votes
2
replies
5.0k
views
Ensembl site unresponsive, trying uswest mirror
GenomicVariantsWorkflow
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
4
replies
2.9k
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Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
4.2 years ago Tongjun • 0
1
vote
1
reply
1.4k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.3 years ago • updated 4.2 years ago Mallory ▴ 10
0
votes
1
reply
2.5k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
4.2 years ago william.ho • 0
10
votes
18
replies
4.6k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 4.2 years ago by 16k • written 4.2 years ago by 43k
4
votes
6
replies
2.1k
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RMA on different disease labels
rma background microarray normalization
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
1
reply
1.3k
views
DESeq2 design formula
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
1
vote
5
replies
4.0k
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tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 2.5 years ago by 43k • written 4.2 years ago by • 0
0
votes
2
replies
1.7k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.2 years ago m.glymenaki • 0
5
votes
4
replies
1.3k
views
DESeq2 with multiple variable give me different results
Factor Levels Dispersionestimates DESeq2
4.2 years ago rafaelsolersanblas ▴ 50
1
vote
1
reply
725
views
Mac/Windows test build systems?
build
updated 4.2 years ago by 4.3k • written 4.2 years ago by • 0
0
votes
1
reply
1.0k
views
CopywriteR output
CopywriteR
updated 21 months ago by • 0 • written 4.2 years ago by • 0
0
votes
5
replies
2.1k
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Rcpp mismatch? MzR problem
mzR
updated 4.2 years ago by 1.6k • written 4.2 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 ratio of ratios and p-value
DESeq2 dese
4.2 years ago wilfried.guiblet • 0
1
vote
3
replies
8.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
0
votes
8
replies
2.0k
views
DESeq2 cannot relevel
DESeq2
4.2 years ago Jorge • 0
0
votes
1
reply
1.1k
views
Error in flowCore::read.FCS(): Error in uint2double(splitted, endian == "big") : vector
read.FCS flowCore
4.2 years ago Rainer • 0
3
votes
2
replies
5.2k
views
gseGO input list
clusterProfiler
4.2 years ago leakerb • 0
0
votes
0
replies
1.5k
views
Job: Postdoctoral Scientist in Statistical Bioinformatics, WEHI, Melbourne, Australia
JobPosting
4.2 years ago Yunshun Chen ▴ 900
0
votes
1
reply
1.1k
views
Multiple testing correction for p.scores in FELLA
FELLA
4.2 years ago sergi.picart ▴ 20
46,721 results • Page 108 of 935
Recent ...
Replies
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results by sup0903 • 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Comment: Ensembl site unresponsive via biomaRt by sebastianenewell • 0
> I think this is an unrelated issue. The original post includes the > message Error: 'curl_parse_url' is not an exported object from > 'na…
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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